The Barcode of Life Data Portal: Bridging the Biodiversity Informatics Divide for DNA Barcoding

With the volume of molecular sequence data that is systematically being generated globally, there is a need for centralized resources for data exploration and analytics. DNA Barcode initiatives are on track to generate a compendium of molecular sequence–based signatures for identifying animals and plants. To date, the range of available data exploration and analytic tools to explore these data have only been available in a boutique form—often representing a frustrating hurdle for many researchers that may not necessarily have resources to install or implement algorithms described by the analytic community. The Barcode of Life Data Portal (BDP) is a first step towards integrating the latest biodiversity informatics innovations with molecular sequence data from DNA barcoding. Through establishment of community driven standards, based on discussion with the Data Analysis Working Group (DAWG) of the Consortium for the Barcode of Life (CBOL), the BDP provides an infrastructure for incorporation of existing and next-generation DNA barcode analytic applications in an open forum

Are language and social communication intact in children with congenital visual impairment at school age?

Background:  Development of children with congenital visual impairment (VI) has been associated with vulnerable socio-communicative outcomes often bearing striking similarities to those of sighted children with autism.1 To date, very little is known about language and social communication in children with VI of normal intelligence. Methods:  We examined the presentation of language and social communication of 15 children with VI and normal-range verbal intelligence, age 6–12 years, using a standardised language assessment and parental reports of everyday social and communicative behaviours. Their profiles were compared to those of typically developing sighted children of similar age and verbal ability. Results:  Compared to their sighted peers, and relative to their own good and potentially superior structural language skills, children with VI showed significantly poorer use of language for social purposes. Pragmatic language weaknesses were a part of a broader socio-communicative profile of difficulties, present in a substantial proportion of these children and consistent with the pattern found in sighted children with autism. Conclusions:  There are ongoing socio-communicative and pragmatic language difficulties in children with congenital VI at school age, despite their good intellectual abilities and advanced linguistic skills. Further research is required to unpack the underlying causes and factors maintaining this vulnerability in such children

Human Intestinal Cells Modulate Conjugational Transfer of Multidrug Resistance Plasmids between Clinical Escherichia coli Isolates.

Bacterial conjugation in the human gut microbiota is believed to play a major role in the dissemination of antibiotic resistance genes and virulence plasmids. However, the modulation of bacterial conjugation by the human host remains poorly understood and there is a need for controlled systems to study this process. We established an in vitro co-culture system to study the interaction between human intestinal cells and bacteria. We show that the conjugation efficiency of a plasmid encoding an extended spectrum beta-lactamase is reduced when clinical isolates of Escherichia coli are co-cultured with human intestinal cells. We show that filtered media from co-cultures contain a factor that reduces conjugation efficiency. Protease treatment of the filtered media eliminates this inhibition of conjugation. This data suggests that a peptide or protein based factor is secreted on the apical side of the intestinal cells exposed to bacteria leading to a two-fold reduction in conjugation efficiency. These results show that human gut epithelial cells can modulate bacterial conjugation and may have relevance to gene exchange in the gut

Reduction of Dopamine Level Enhances the Attractiveness of Male Drosophila to Other Males

Dopamine is an important neuromodulator in animals and its roles in mammalian sexual behavior are extensively studied. Drosophila as a useful model system is widely used in many fields of biological studies. It has been reported that dopamine reduction can affect female receptivity in Drosophila and leave male-female courtship behavior unaffected. Here, we used genetic and pharmacological approaches to decrease the dopamine level in dopaminergic cells in Drosophila, and investigated the consequence of this manipulation on male homosexual courtship behavior. We find that reduction of dopamine level can induce Drosophila male-male courtship behavior, and that this behavior is mainly due to the increased male attractiveness or decreased aversiveness towards other males, but not to their enhanced propensity to court other males. Chemical signal input probably plays a crucial role in the male-male courtship induced by the courtees with reduction of dopamine. Our finding provides insight into the relationship between the dopamine reduction and male-male courtship behavior, and hints dopamine level is important for controlling Drosophila courtship behavior

Survivability Is More Fundamental Than Evolvability

For a lineage to survive over long time periods, it must sometimes change. This has given rise to the term evolvability, meaning the tendency to produce adaptive variation. One lineage may be superior to another in terms of its current standing variation, or it may tend to produce more adaptive variation. However, evolutionary outcomes depend on more than standing variation and produced adaptive variation: deleterious variation also matters. Evolvability, as most commonly interpreted, is not predictive of evolutionary outcomes. Here, we define a predictive measure of the evolutionary success of a lineage that we call the k-survivability, defined as the probability that the lineage avoids extinction for k generations. We estimate the k-survivability using multiple experimental replicates. Because we measure evolutionary outcomes, the initial standing variation, the full spectrum of generated variation, and the heritability of that variation are all incorporated. Survivability also accounts for the decreased joint likelihood of extinction of sub-lineages when they 1) disperse in space, or 2) diversify in lifestyle. We illustrate measurement of survivability with in silico models, and suggest that it may also be measured in vivo using multiple longitudinal replicates. The k-survivability is a metric that enables the quantitative study of, for example, the evolution of 1) mutation rates, 2) dispersal mechanisms, 3) the genotype-phenotype map, and 4) sexual reproduction, in temporally and spatially fluctuating environments. Although these disparate phenomena evolve by well-understood microevolutionary rules, they are also subject to the macroevolutionary constraint of long-term survivability

Advanced Genomic Data Mining

As data banks increase their size, one of the current challenges in bioinformatics is to be able to query them in a sensible way. Information is contained in differen

The development of a protoplanetary disk from its natal envelope

Class 0 protostars, the youngest type of young stellar objects, show many signs of rapid development from their initial, spheroidal configurations, and therefore are studied intensively for details of the formation of protoplanetary disks within protostellar envelopes. At millimetre wavelengths, kinematic signatures of collapse have been observed in several such protostars, through observations of molecular lines that probe their outer envelopes. It has been suggested that one or more components of the proto-multiple system NGC 1333-IRAS 4 (refs 1, 2) may display signs of an embedded region that is warmer and denser than the bulk of the envelope(3,4). Here we report observations that reveal details of the core on Solar System dimensions. We detect in NGC 1333-IRAS 4B a rich emission spectrum of H2O, at wavelengths 20-37 mu m, which indicates an origin in extremely dense, warm gas. We can model the emission as infall from a protostellar envelope onto the surface of a deeply embedded, dense disk, and therefore see the development of a protoplanetary disk. This is the only example of mid-infrared water emission from a sample of 30 class 0 objects, perhaps arising from a favourable orientation; alternatively, this may be an early and short-lived stage in the evolution of a protoplanetary disk.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62894/1/nature06087.pd

Fire performance of sandwich panels in a modified ISO 13784-1 small room test: the influence of increased fire load for different insulation materials

Four sandwich panel rooms were constructed as prescribed in the ISO 13784-1 test. However, the construction followed normal industry practice, and the panels were also subjected to the kinds of damage typically found in commercial premises, although such damage may not typically be concentrated in such a small room. The fire load was increased to simulate fires actually occurring in commercial premises by stepping up the propane burner output from the usual maximum of 300–600 kW, and by placing a substantial wooden crib in two of the rooms. The results showed significant differences in fire growth rate and burning behaviour between those panels filled with polyisocyanurate (PIR) and those filled with stone wool in both the experiments without and with the wooden crib. Most significantly, the PIR pyrolysis products caused earlier ignition (by radiation from above) of the wooden crib 11 min into the experiment (1 min after the burner was stepped up to 300 kW), whereas the crib ignited 22 min into the test (2 min after the burner had been stepped up to 600 kW, which is beyond the test standard both in time and heat input) for the stone wool panels. This interaction between building and contents is most often ignored in fire safety assessments. After a few minutes, the PIR pyrolysis products that escaped outside the room, from between the panels, ignited. The extra thermal exposure from the PIR-fuelled flames distorted the panels, which in turn exposed more PIR, resulting in large flames on both the inside and outside of the enclosure. From a fire safety perspective this is most important as it shows that with the large fire loads that are commonly found in commercial premises, steel-faced PIR filled panels are not capable of acting as fire barriers, and may support flame spread through compartment walls and ceilings. In addition, the PIR panelled rooms produced very large quantities of dense smoke and toxic effluents, whereas the stone wool panelled rooms produced small amounts of light smoke of lower toxicity. Furthermore, the experiments showed that modifications to the standard test can lead to extremely different outcomes for some of the products. As the modifications simulated real-life situations, it seems important to discuss whether the standard is robust enough for property safety scenarios encountered in industrial premises

The fire toxicity of polyurethane foams [Review]

Polyurethane is widely used, with its two major applications, soft furnishings and insulation, having low thermal inertia, and hence enhanced flammability. In addition to their flammability, polyurethanes form carbon monoxide, hydrogen cyanide and other toxic products on decomposition and combustion. The chemistry of polyurethane foams and their thermal decomposition are discussed in order to assess the relationship between the chemical and physical composition of the foam and the toxic products generated during their decomposition. The toxic product generation during flaming combustion of polyurethane foams is reviewed, in order to relate the yields of toxic products and the overall fire toxicity to the fire conditions. The methods of assessment of fire toxicity are outlined in order to understand how the fire toxicity of polyurethane foams may be quantified. In particular, the ventilation condition has a critical effect on the yield of the two major asphyxiants, carbon monoxide and hydrogen cyanid